Parameters Input values
Folder name : Example data
Sequence name : Test sequence
Reference genome : BSgenome.Hsapiens.UCSC.hg19
Type of experiment : Direct-BSP
Group order : group1, group2
Date of analysis : 2022-05-18 13:03

Files content

Data files content

Parameters Data files content
Sequence name : Test sequence
Collections : collection1, collection2
Groups : group1, group2
Replicates : 1, 2, 3

Data files paths

File paths used for the analysis

D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group1_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group1_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group1_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group2_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group2_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group2_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group1_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group1_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group1_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group2_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group2_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group2_3_methdata.csv

Methylation data

Methylation data of replicates

chr16:68770595-68770596 chr16:68770613-68770614 chr16:68770646-68770647 chr16:68770665-68770666 chr16:68770670-68770671 chr16:68770717-68770718 Mean SD
collection1 group1 1 38.44 21.17 5.56 24.31 0.00 12.61 17.02 13.93
collection1 group1 2 18.65 12.84 16.93 19.07 0.00 20.09 14.60 7.59
collection1 group1 3 6.12 8.25 24.85 6.69 32.95 16.63 15.92 11.05
collection1 group2 1 67.41 83.83 84.18 85.67 100.00 74.04 82.52 11.14
collection1 group2 2 55.41 75.91 60.26 52.01 100.00 67.33 68.49 17.66
collection1 group2 3 98.62 65.18 56.78 82.81 70.73 90.10 77.37 15.87
collection2 group1 1 21.60 13.38 24.98 31.74 4.84 20.58 19.52 9.36
collection2 group1 2 38.62 0.00 52.73 16.17 36.61 0.00 24.02 21.96
collection2 group1 3 19.37 3.66 43.99 4.87 33.12 25.27 21.71 15.84
collection2 group2 1 61.26 63.68 83.57 71.25 56.68 93.89 71.72 14.37
collection2 group2 2 62.96 91.07 86.62 61.63 78.68 80.02 76.83 12.13
collection2 group2 3 72.37 65.22 70.84 82.10 81.23 66.92 73.11 7.11

Methylation data of groups

chr16:68770595-68770596 chr16:68770613-68770614 chr16:68770646-68770647 chr16:68770665-68770666 chr16:68770670-68770671 chr16:68770717-68770718 Mean SD
collection1 group1 21.07 14.09 15.78 16.69 10.98 16.44 15.84 3.32
collection1 group2 73.81 74.97 67.07 73.50 90.24 77.16 76.12 7.69
collection2 group1 26.53 5.68 40.57 17.59 24.86 15.28 21.75 11.87
collection2 group2 65.53 73.32 80.34 71.66 72.20 80.28 73.89 5.67

Plots of replicates

Lollipop plots

Sample order : as-is

Type : proportional

Type : condensed

Sample order : by-group

Type : proportional

Type : condensed

Sample order : by-meth

Type : proportional

Type : condensed

Sample order : clust

Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Sample order : by-group

Sample order : by-meth

Sample order : clust

Plots of groups

Lollipop plots

Sample order : as-is

Type : proportional

Type : condensed

Sample order : by-group

Type : proportional

Type : condensed

Sample order : by-meth

Type : proportional

Type : condensed

Sample order : clust

Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Sample order : by-group

Sample order : by-meth

Sample order : clust

Statistics

Descriptive statistics of groups

Methylation by CpG positions

CpG number CpG coordinate Collection Group N Methylation mean SD SEM Confidence interval of 95% (±)
1 chr16:68770595-68770596 collection1 group1 3 21.07 16.30 9.41 40.48
1 chr16:68770595-68770596 collection1 group2 3 73.81 22.31 12.88 55.41
1 chr16:68770595-68770596 collection2 group1 3 26.53 10.53 6.08 26.16
1 chr16:68770595-68770596 collection2 group2 3 65.53 5.98 3.46 14.87
2 chr16:68770613-68770614 collection1 group1 3 14.09 6.55 3.78 16.27
2 chr16:68770613-68770614 collection1 group2 3 74.97 9.36 5.40 23.25
2 chr16:68770613-68770614 collection2 group1 3 5.68 6.91 3.99 17.18
2 chr16:68770613-68770614 collection2 group2 3 73.32 15.39 8.88 38.23
3 chr16:68770646-68770647 collection1 group1 3 15.78 9.70 5.60 24.09
3 chr16:68770646-68770647 collection1 group2 3 67.07 14.92 8.61 37.05
3 chr16:68770646-68770647 collection2 group1 3 40.57 14.19 8.19 35.25
3 chr16:68770646-68770647 collection2 group2 3 80.34 8.37 4.83 20.79
4 chr16:68770665-68770666 collection1 group1 3 16.69 9.05 5.22 22.48
4 chr16:68770665-68770666 collection1 group2 3 73.50 18.66 10.78 46.36
4 chr16:68770665-68770666 collection2 group1 3 17.59 13.49 7.79 33.51
4 chr16:68770665-68770666 collection2 group2 3 71.66 10.24 5.91 25.44
5 chr16:68770670-68770671 collection1 group1 3 10.98 19.02 10.98 47.26
5 chr16:68770670-68770671 collection1 group2 3 90.24 16.90 9.76 41.98
5 chr16:68770670-68770671 collection2 group1 3 24.86 17.42 10.06 43.28
5 chr16:68770670-68770671 collection2 group2 3 72.20 13.50 7.79 33.53
6 chr16:68770717-68770718 collection1 group1 3 16.44 3.74 2.16 9.30
6 chr16:68770717-68770718 collection1 group2 3 77.16 11.70 6.76 29.07
6 chr16:68770717-68770718 collection2 group1 3 15.28 13.44 7.76 33.39
6 chr16:68770717-68770718 collection2 group2 3 80.28 13.49 7.79 33.50

Methylation means of all CpG positions

Collection Group N Methylation mean SD SEM Confidence interval of 95% (±)
collection1 group1 3 15.85 1.21 0.70 3.01
collection1 group2 3 76.13 7.10 4.10 17.63
collection2 group1 3 21.75 2.25 1.30 5.59
collection2 group2 3 73.89 2.64 1.53 6.56

Student’s T test

For each CpG position

Student’s T test (two-samples, unpaired)

CpG number CpG coordinate Collection Compared group 1 Compared group 2 N group 1 N group 2 p-value p-value significance level
1 chr16:68770595-68770596 collection1 group1 group2 3 3 0.03390 *
2 chr16:68770613-68770614 collection1 group1 group2 3 3 0.00127 **
3 chr16:68770646-68770647 collection1 group1 group2 3 3 0.01110 *
4 chr16:68770665-68770666 collection1 group1 group2 3 3 0.01930 *
5 chr16:68770670-68770671 collection1 group1 group2 3 3 0.00594 **
6 chr16:68770717-68770718 collection1 group1 group2 3 3 0.00741 **
1 chr16:68770595-68770596 collection2 group1 group2 3 3 0.00981 **
2 chr16:68770613-68770614 collection2 group1 group2 3 3 0.00784 **
3 chr16:68770646-68770647 collection2 group1 group2 3 3 0.02140 *
4 chr16:68770665-68770666 collection2 group1 group2 3 3 0.00640 **
5 chr16:68770670-68770671 collection2 group1 group2 3 3 0.02280 *
6 chr16:68770717-68770718 collection2 group1 group2 3 3 0.00410 **

For means of CpG positions

Student’s T test (two-samples, unpaired)

Collection Compared group 1 Compared group 2 N group 1 N group 2 p-value p-value significance level
collection1 group1 group2 3 3 3.74e-03 **
collection2 group1 group2 3 3 1.61e-05 ****

Boxplots

For each CpG position

Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.

The p-values and p-value significance levels are determined by Student’s T tests (unpaired).

p-values

p-values significance levels

For means of CpG positions

Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.

The p-values and p-value significance levels are determined by Student’s T tests (unpaired).

p-values

p-values significance levels

Methylation profile plots

Each points represent the methylation mean of clones or replicates for a given CpG site.
The p-values and p-value significance levels are determined by Kruskal-Wallis tests.

collection1

Type : proportional
p-values

p-values significance levels

Type : condensed
p-values

p-values significance levels

collection2

Type : proportional
p-values

p-values significance levels

Type : condensed
p-values

p-values significance levels

Output data

Directories

Files